Merge pull request #364 from jo-basevi/325-read-mom6-parameter-filenames

Read MOM6 parameter filenames defined in input.nml

payu/models/mom6.py

@@ -10,6 +10,7 @@
 
 # Standard library
 import os
+import shutil
 
 # Extensions
 import f90nml
@@ -31,34 +32,20 @@ def __init__(self, expt, name, config):
 
         self.config_files = [
             'input.nml',
-            'MOM_input',
             'diag_table',
         ]
 
-        # TODO: Need to figure out what's going on here with MOM6
         self.optional_config_files = [
             'data_table',
-            'data_table.MOM6',
-            'data_table.OM4',
-            'data_table.SIS',
-            'data_table.icebergs',
-
-            'field_table',
-
-            'MOM_override',
-            'MOM_layout',
-            'MOM_saltrestore',
-
-            'SIS_input',
-            'SIS_override',
-            'SIS_layout',
+            'field_table'
         ]
 
     def setup(self):
         # FMS initialisation
         super(Mom6, self).setup()
 
         self.init_config()
+        self.add_config_files()
 
     def init_config(self):
         """Patch input.nml as a new or restart run."""
@@ -78,3 +65,47 @@ def init_config(self):
             input_nml['SIS_input_nml']['input_filename'] = input_type
 
         f90nml.write(input_nml, input_fpath, force=True)
+
+    def add_config_files(self):
+        """Add to model configuration files"""
+
+        # Add parameter config files
+        config_files_to_add = self.get_parameter_files()
+
+        # Set of all configuration files
+        all_config_files = set(self.config_files).union(
+            self.optional_config_files)
+
+        for filename in config_files_to_add:
+            if filename not in all_config_files:
+                # Extend config files
+                self.config_files.append(filename)
+                all_config_files.add(filename)
+
+                # Copy file from control path to work path
+                file_path = os.path.join(self.control_path, filename)
+                shutil.copy(file_path, self.work_path)
+
+    def get_parameter_files(self):
+        """Return a list of parameter config files defined in input.nml"""
+        input_nml = f90nml.read(os.path.join(self.work_path, 'input.nml'))
+
+        input_namelists = ['MOM_input_nml']
+        if 'SIS_input_nml' in input_nml:
+            input_namelists.append('SIS_input_nml')
+
+        parameter_files = []
+        for input in input_namelists:
+            input_namelist = input_nml.get(input, {})
+            filenames = input_namelist.get('parameter_filename', [])
+
+            if filenames == []:
+                print("payu: warning: MOM6: There are no parameter files "
+                      f"listed under {input} in input.nml")
+
+            if isinstance(filenames, str):
+                parameter_files.append(filenames)
+            else:
+                parameter_files.extend(filenames)
+
+        return parameter_files

test/common.py

@@ -13,13 +13,17 @@
 from payu.subcommands.setup_cmd import runcmd as payu_setup_orignal
 from payu.subcommands.sweep_cmd import runcmd as payu_sweep
 
+ctrldir_basename = 'ctrl'
+
 testdir = Path().cwd() / Path('test')
 tmpdir = testdir / 'tmp'
-ctrldir = tmpdir / 'ctrl'
+ctrldir = tmpdir / ctrldir_basename
 labdir = tmpdir / 'lab'
 workdir = ctrldir / 'work'
 payudir = tmpdir / 'payu'
 
+expt_workdir = labdir / 'work' / ctrldir_basename
+
 print('tmpdir: {}'.format(tmpdir))
 
 config = {
@@ -43,6 +47,7 @@
                         }
             }
 
+
 @contextmanager
 def cd(directory):
     """

test/models/test_mom6.py

@@ -0,0 +1,134 @@
+import copy
+import os
+import shutil
+
+import pytest
+import f90nml
+
+import payu
+
+from test.common import cd
+from test.common import tmpdir, ctrldir, labdir, expt_workdir
+from test.common import config as config_orig
+from test.common import write_config
+from test.common import make_random_file, make_inputs
+
+verbose = True
+
+# Global config
+config = copy.deepcopy(config_orig)
+config["model"] = "mom6"
+
+
+def setup_module(module):
+    """
+    Put any test-wide setup code in here, e.g. creating test files
+    """
+    if verbose:
+        print("setup_module      module:%s" % module.__name__)
+
+    # Should be taken care of by teardown, in case remnants lying around
+    try:
+        shutil.rmtree(tmpdir)
+    except FileNotFoundError:
+        pass
+
+    try:
+        tmpdir.mkdir()
+        labdir.mkdir()
+        ctrldir.mkdir()
+        expt_workdir.mkdir(parents=True)
+        make_inputs()
+    except Exception as e:
+        print(e)
+
+    write_config(config)
+
+
+def teardown_module(module):
+    """
+    Put any test-wide teardown code in here, e.g. removing test outputs
+    """
+    if verbose:
+        print("teardown_module   module:%s" % module.__name__)
+
+    try:
+        shutil.rmtree(tmpdir)
+        print('removing tmp')
+    except Exception as e:
+        print(e)
+
+
+@pytest.fixture(autouse=True)
+def teardown():
+    # Run test
+    yield
+
+    # Remove any files in expt work directory
+    for file in os.listdir(expt_workdir):
+        try:
+            os.remove(os.path.join(expt_workdir, file))
+        except Exception as e:
+            print(e)
+
+
+@pytest.mark.parametrize(
+        "input_nml, expected_files_added",
+        [
+            (
+                {
+                    "MOM_input_nml": {
+                        "parameter_filename": "MOM_Input"
+                    }
+                },
+                ["MOM_Input"]
+            ),
+            (
+                {
+                    "SIS_input_nml": {
+                        "parameter_filename": "SIS_Input"
+                    }
+                },
+                ["SIS_Input"]
+            ),
+            (
+                {
+                    "MOM_input_nml": {
+                        "parameter_filename": ["MOM_Input", "MOM_override"]
+                    },
+                    "SIS_input_nml": {
+                        "output_directory": '.'
+                    }
+                },
+                ["MOM_Input", "MOM_override"]
+            )
+        ])
+def test_add_config_files(input_nml,
+                          expected_files_added):
+    # Create config files in control directory
+    for file in expected_files_added:
+        filename = os.path.join(ctrldir, file)
+        make_random_file(filename, 8)
+
+    # Create config.nml
+    input_nml_fp = os.path.join(expt_workdir, 'input.nml')
+    f90nml.write(input_nml, input_nml_fp)
+
+    with cd(ctrldir):
+        lab = payu.laboratory.Laboratory(lab_path=str(labdir))
+        expt = payu.experiment.Experiment(lab, reproduce=False)
+        model = expt.models[0]
+
+    prior_config_files = model.config_files[:]
+
+    # Function to test
+    model.add_config_files()
+
+    # Check files are added to config_files
+    added_files = set(model.config_files).difference(prior_config_files)
+    assert added_files == set(expected_files_added)
+
+    # Check the extra files are moved to model's work path
+    ctrl_path_files = os.listdir(model.work_path)
+    for file in expected_files_added:
+        assert file in ctrl_path_files